1-113834340-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000359785.10(PTPN22):c.1994T>C(p.Phe665Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,614,028 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000359785.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.1994T>C | p.Phe665Ser | missense_variant | 15/21 | ENST00000359785.10 | |
PTPN22 | XM_047417630.1 | c.1844T>C | p.Phe615Ser | missense_variant | 13/19 | ||
AP4B1-AS1 | NR_125965.1 | n.414+18868A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN22 | ENST00000359785.10 | c.1994T>C | p.Phe665Ser | missense_variant | 15/21 | 1 | NM_015967.8 | P1 | |
ENST00000664434.1 | n.470+2527A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251390Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135876
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461740Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727178
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152288Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74462
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at